Re: Keeping rigidBonds during Minimization

From: Jérôme Hénin (
Date: Mon Sep 12 2011 - 18:09:58 CDT

Hi Dave,

Someone will correct me if I am wrong, but my understanding is that
NAMD does not implement constrained minimization. The closest you can
get to that is bonded terms very high force constants (which won't
cause the stability issues that they would in MD). Usually this is not
necessary because bonded terms in water molecules dominate nonbonded
terms, so the energy-minimized geometry is very close to the ideal
one. Now maybe close is not close enough, in your particular case.
Also, my experience is with TIP3P only - TIP4P may be softer.


On 12 September 2011 19:20, David Huggins <> wrote:
> Dear All,
> I cannot seem to solve this problem. When I run MD with TIP4P water
> and rigidBonds all, the water geometries all remain constant from step to
> step. However, when I attempt to minimize with TIP4P water
> and rigidBonds all, the water geometries change.
> Is it possible to minimize and keep waters rigid?
> Thanks,
> Dave
> On 1 September 2011 01:05, David Huggins <> wrote:
>> Dear All,
>> I am simulating TIP4P waters with NAMD (using watermodel tip4). When I
>> attempy to minimize (with rigidBonds all or water) the water OH distances
>> and the HOH angle change.
>> What are the correct options and settings to ensure that these distances
>> and angles are fixed during minimization?
>> Thanks,
>> Dave

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